@velvetmonkey/flywheel-memory 2.0.119 → 2.0.121

package/dist/index.js

@@ -128,17 +128,23 @@ var init_levenshtein = __esm({
 });
 
 // src/vault-scope.ts
+import { AsyncLocalStorage } from "node:async_hooks";
 function getActiveScopeOrNull() {
-  return activeScope;
+  return vaultAls.getStore() ?? fallbackScope;
 }
-function setActiveScope(scope) {
-  activeScope = scope;
+function runInVaultScope(scope, fn) {
+  return vaultAls.run(scope, fn);
 }
-var activeScope;
+function setFallbackScope(scope) {
+  fallbackScope = scope;
+}
+var vaultAls, fallbackScope, setActiveScope;
 var init_vault_scope = __esm({
   "src/vault-scope.ts"() {
     "use strict";
-    activeScope = null;
+    vaultAls = new AsyncLocalStorage();
+    fallbackScope = null;
+    setActiveScope = setFallbackScope;
   }
 });
 
@@ -155,14 +161,22 @@ function getModelConfig() {
 function getActiveModelId() {
   return activeModelConfig.id;
 }
+function getDb() {
+  return getActiveScopeOrNull()?.stateDb?.db ?? db;
+}
+function getEmbMap() {
+  return getActiveScopeOrNull()?.entityEmbeddingsMap ?? entityEmbeddingsMap;
+}
 function getEmbeddingsBuildState() {
-  if (!db) return "none";
-  const row = db.prepare(`SELECT value FROM fts_metadata WHERE key = 'embeddings_state'`).get();
+  const db4 = getDb();
+  if (!db4) return "none";
+  const row = db4.prepare(`SELECT value FROM fts_metadata WHERE key = 'embeddings_state'`).get();
   return row?.value || "none";
 }
 function setEmbeddingsBuildState(state2) {
-  if (!db) return;
-  db.prepare(`INSERT OR REPLACE INTO fts_metadata (key, value) VALUES ('embeddings_state', ?)`).run(state2);
+  const db4 = getDb();
+  if (!db4) return;
+  db4.prepare(`INSERT OR REPLACE INTO fts_metadata (key, value) VALUES ('embeddings_state', ?)`).run(state2);
 }
 function setEmbeddingsDatabase(database) {
   db = database;
@@ -273,7 +287,8 @@ function shouldIndexFile(filePath) {
   return !parts.some((part) => EXCLUDED_DIRS2.has(part));
 }
 async function buildEmbeddingsIndex(vaultPath2, onProgress) {
-  if (!db) {
+  const db4 = getDb();
+  if (!db4) {
     throw new Error("Embeddings database not initialized. Call setEmbeddingsDatabase() first.");
   }
   embeddingsBuilding = true;
@@ -282,11 +297,11 @@ async function buildEmbeddingsIndex(vaultPath2, onProgress) {
   const files = await scanVault(vaultPath2);
   const indexable = files.filter((f) => shouldIndexFile(f.path));
   const existingHashes = /* @__PURE__ */ new Map();
-  const rows = db.prepare("SELECT path, content_hash FROM note_embeddings").all();
+  const rows = db4.prepare("SELECT path, content_hash FROM note_embeddings").all();
   for (const row of rows) {
     existingHashes.set(row.path, row.content_hash);
   }
-  const upsert = db.prepare(`
+  const upsert = db4.prepare(`
     INSERT OR REPLACE INTO note_embeddings (path, embedding, content_hash, model, updated_at)
     VALUES (?, ?, ?, ?, ?)
   `);
@@ -318,7 +333,7 @@ async function buildEmbeddingsIndex(vaultPath2, onProgress) {
     if (onProgress) onProgress(progress);
   }
   const currentPaths = new Set(indexable.map((f) => f.path));
-  const deleteStmt = db.prepare("DELETE FROM note_embeddings WHERE path = ?");
+  const deleteStmt = db4.prepare("DELETE FROM note_embeddings WHERE path = ?");
   for (const existingPath of existingHashes.keys()) {
     if (!currentPaths.has(existingPath)) {
       deleteStmt.run(existingPath);
@@ -329,15 +344,16 @@ async function buildEmbeddingsIndex(vaultPath2, onProgress) {
   return progress;
 }
 async function updateEmbedding(notePath, absolutePath) {
-  if (!db) return;
+  const db4 = getDb();
+  if (!db4) return;
   try {
     const content = fs3.readFileSync(absolutePath, "utf-8");
     const hash = contentHash(content);
-    const existing = db.prepare("SELECT content_hash FROM note_embeddings WHERE path = ?").get(notePath);
+    const existing = db4.prepare("SELECT content_hash FROM note_embeddings WHERE path = ?").get(notePath);
     if (existing?.content_hash === hash) return;
     const embedding = await embedText(content);
     const buf = Buffer.from(embedding.buffer, embedding.byteOffset, embedding.byteLength);
-    db.prepare(`
+    db4.prepare(`
       INSERT OR REPLACE INTO note_embeddings (path, embedding, content_hash, model, updated_at)
       VALUES (?, ?, ?, ?, ?)
     `).run(notePath, buf, hash, activeModelConfig.id, Date.now());
@@ -345,8 +361,9 @@ async function updateEmbedding(notePath, absolutePath) {
   }
 }
 function removeEmbedding(notePath) {
-  if (!db) return;
-  db.prepare("DELETE FROM note_embeddings WHERE path = ?").run(notePath);
+  const db4 = getDb();
+  if (!db4) return;
+  db4.prepare("DELETE FROM note_embeddings WHERE path = ?").run(notePath);
 }
 function cosineSimilarity(a, b) {
   let dot = 0;
@@ -362,11 +379,12 @@ function cosineSimilarity(a, b) {
   return dot / denom;
 }
 async function semanticSearch(query, limit = 10) {
-  if (!db) {
+  const db4 = getDb();
+  if (!db4) {
     throw new Error("Embeddings database not initialized. Call setEmbeddingsDatabase() first.");
   }
   const queryEmbedding = await embedText(query);
-  const rows = db.prepare("SELECT path, embedding FROM note_embeddings").all();
+  const rows = db4.prepare("SELECT path, embedding FROM note_embeddings").all();
   const scored = [];
   for (const row of rows) {
     const noteEmbedding = new Float32Array(
@@ -382,10 +400,11 @@ async function semanticSearch(query, limit = 10) {
   return scored.slice(0, limit);
 }
 async function findSemanticallySimilar(sourcePath, limit = 10, excludePaths) {
-  if (!db) {
+  const db4 = getDb();
+  if (!db4) {
     throw new Error("Embeddings database not initialized. Call setEmbeddingsDatabase() first.");
   }
-  const sourceRow = db.prepare("SELECT embedding FROM note_embeddings WHERE path = ?").get(sourcePath);
+  const sourceRow = db4.prepare("SELECT embedding FROM note_embeddings WHERE path = ?").get(sourcePath);
   if (!sourceRow) {
     return [];
   }
@@ -394,7 +413,7 @@ async function findSemanticallySimilar(sourcePath, limit = 10, excludePaths) {
     sourceRow.embedding.byteOffset,
     sourceRow.embedding.byteLength / Float32Array.BYTES_PER_ELEMENT
   );
-  const rows = db.prepare("SELECT path, embedding FROM note_embeddings WHERE path != ?").all(sourcePath);
+  const rows = db4.prepare("SELECT path, embedding FROM note_embeddings WHERE path != ?").all(sourcePath);
   const scored = [];
   for (const row of rows) {
     if (excludePaths?.has(row.path)) continue;
@@ -430,12 +449,13 @@ function setEmbeddingsBuilding(value) {
   embeddingsBuilding = value;
 }
 function hasEmbeddingsIndex() {
-  if (!db) return false;
+  const db4 = getDb();
+  if (!db4) return false;
   try {
     const state2 = getEmbeddingsBuildState();
     if (state2 === "complete") return true;
     if (state2 === "none") {
-      const row = db.prepare("SELECT COUNT(*) as count FROM note_embeddings").get();
+      const row = db4.prepare("SELECT COUNT(*) as count FROM note_embeddings").get();
       return row.count > 0;
     }
     return false;
@@ -444,9 +464,10 @@ function hasEmbeddingsIndex() {
   }
 }
 function getStoredEmbeddingModel() {
-  if (!db) return null;
+  const db4 = getDb();
+  if (!db4) return null;
   try {
-    const row = db.prepare("SELECT model FROM note_embeddings LIMIT 1").get();
+    const row = db4.prepare("SELECT model FROM note_embeddings LIMIT 1").get();
     return row?.model ?? null;
   } catch {
     return null;
@@ -458,19 +479,21 @@ function needsEmbeddingRebuild() {
   return stored !== activeModelConfig.id;
 }
 function getEmbeddingsCount() {
-  if (!db) return 0;
+  const db4 = getDb();
+  if (!db4) return 0;
   try {
-    const row = db.prepare("SELECT COUNT(*) as count FROM note_embeddings").get();
+    const row = db4.prepare("SELECT COUNT(*) as count FROM note_embeddings").get();
     return row.count;
   } catch {
     return 0;
   }
 }
 function loadAllNoteEmbeddings() {
+  const db4 = getDb();
   const result = /* @__PURE__ */ new Map();
-  if (!db) return result;
+  if (!db4) return result;
   try {
-    const rows = db.prepare("SELECT path, embedding FROM note_embeddings").all();
+    const rows = db4.prepare("SELECT path, embedding FROM note_embeddings").all();
     for (const row of rows) {
       const embedding = new Float32Array(
         row.embedding.buffer,
@@ -500,17 +523,18 @@ function buildEntityEmbeddingText(entity, vaultPath2) {
   return parts.join(" ");
 }
 async function buildEntityEmbeddingsIndex(vaultPath2, entities, onProgress) {
-  if (!db) {
+  const db4 = getDb();
+  if (!db4) {
     throw new Error("Embeddings database not initialized. Call setEmbeddingsDatabase() first.");
   }
   await initEmbeddings();
   setEmbeddingsBuildState("building_entities");
   const existingHashes = /* @__PURE__ */ new Map();
-  const rows = db.prepare("SELECT entity_name, source_hash FROM entity_embeddings").all();
+  const rows = db4.prepare("SELECT entity_name, source_hash FROM entity_embeddings").all();
   for (const row of rows) {
     existingHashes.set(row.entity_name, row.source_hash);
   }
-  const upsert = db.prepare(`
+  const upsert = db4.prepare(`
     INSERT OR REPLACE INTO entity_embeddings (entity_name, embedding, source_hash, model, updated_at)
     VALUES (?, ?, ?, ?, ?)
   `);
@@ -534,7 +558,7 @@ async function buildEntityEmbeddingsIndex(vaultPath2, entities, onProgress) {
     }
     if (onProgress) onProgress(done, total);
   }
-  const deleteStmt = db.prepare("DELETE FROM entity_embeddings WHERE entity_name = ?");
+  const deleteStmt = db4.prepare("DELETE FROM entity_embeddings WHERE entity_name = ?");
   for (const existingName of existingHashes.keys()) {
     if (!entities.has(existingName)) {
       deleteStmt.run(existingName);
@@ -544,15 +568,16 @@ async function buildEntityEmbeddingsIndex(vaultPath2, entities, onProgress) {
   return updated;
 }
 async function updateEntityEmbedding(entityName, entity, vaultPath2) {
-  if (!db) return;
+  const db4 = getDb();
+  if (!db4) return;
   try {
     const text = buildEntityEmbeddingText(entity, vaultPath2);
     const hash = contentHash(text);
-    const existing = db.prepare("SELECT source_hash FROM entity_embeddings WHERE entity_name = ?").get(entityName);
+    const existing = db4.prepare("SELECT source_hash FROM entity_embeddings WHERE entity_name = ?").get(entityName);
     if (existing?.source_hash === hash) return;
     const embedding = await embedTextCached(text);
     const buf = Buffer.from(embedding.buffer, embedding.byteOffset, embedding.byteLength);
-    db.prepare(`
+    db4.prepare(`
       INSERT OR REPLACE INTO entity_embeddings (entity_name, embedding, source_hash, model, updated_at)
       VALUES (?, ?, ?, ?, ?)
     `).run(entityName, buf, hash, activeModelConfig.id, Date.now());
@@ -562,7 +587,7 @@ async function updateEntityEmbedding(entityName, entity, vaultPath2) {
 }
 function findSemanticallySimilarEntities(queryEmbedding, limit, excludeEntities) {
   const scored = [];
-  for (const [entityName, embedding] of entityEmbeddingsMap) {
+  for (const [entityName, embedding] of getEmbMap()) {
     if (excludeEntities?.has(entityName)) continue;
     const similarity = cosineSimilarity(queryEmbedding, embedding);
     scored.push({ entityName, similarity: Math.round(similarity * 1e3) / 1e3 });
@@ -571,12 +596,16 @@ function findSemanticallySimilarEntities(queryEmbedding, limit, excludeEntities)
   return scored.slice(0, limit);
 }
 function hasEntityEmbeddingsIndex() {
-  return entityEmbeddingsMap.size > 0;
+  return getEmbMap().size > 0;
+}
+function getEntityEmbeddingsMap() {
+  return entityEmbeddingsMap;
 }
 function loadEntityEmbeddingsToMemory() {
-  if (!db) return;
+  const db4 = getDb();
+  if (!db4) return;
   try {
-    const rows = db.prepare("SELECT entity_name, embedding FROM entity_embeddings").all();
+    const rows = db4.prepare("SELECT entity_name, embedding FROM entity_embeddings").all();
     entityEmbeddingsMap.clear();
     for (const row of rows) {
       const embedding = new Float32Array(
@@ -593,10 +622,11 @@ function loadEntityEmbeddingsToMemory() {
   }
 }
 function loadNoteEmbeddingsForPaths(paths) {
+  const db4 = getDb();
   const result = /* @__PURE__ */ new Map();
-  if (!db || paths.length === 0) return result;
+  if (!db4 || paths.length === 0) return result;
   try {
-    const stmt = db.prepare("SELECT path, embedding FROM note_embeddings WHERE path = ?");
+    const stmt = db4.prepare("SELECT path, embedding FROM note_embeddings WHERE path = ?");
     for (const p of paths) {
       const row = stmt.get(p);
       if (row) {
@@ -613,12 +643,13 @@ function loadNoteEmbeddingsForPaths(paths) {
   return result;
 }
 function getEntityEmbedding(entityName) {
-  return entityEmbeddingsMap.get(entityName) ?? null;
+  return getEmbMap().get(entityName) ?? null;
 }
 function getEntityEmbeddingsCount() {
-  if (!db) return 0;
+  const db4 = getDb();
+  if (!db4) return 0;
   try {
-    const row = db.prepare("SELECT COUNT(*) as count FROM entity_embeddings").get();
+    const row = db4.prepare("SELECT COUNT(*) as count FROM entity_embeddings").get();
     return row.count;
   } catch {
     return 0;
@@ -1828,6 +1859,9 @@ import {
   recordEntityMention,
   getAllRecency as getAllRecencyFromDb
 } from "@velvetmonkey/vault-core";
+function getStateDb() {
+  return getActiveScopeOrNull()?.stateDb ?? moduleStateDb3;
+}
 function setRecencyStateDb(stateDb2) {
   moduleStateDb3 = stateDb2;
 }
@@ -1898,9 +1932,10 @@ function getRecencyBoost(entityName, index) {
   return 0;
 }
 function loadRecencyFromStateDb() {
-  if (!moduleStateDb3) return null;
+  const stateDb2 = getStateDb();
+  if (!stateDb2) return null;
   try {
-    const rows = getAllRecencyFromDb(moduleStateDb3);
+    const rows = getAllRecencyFromDb(stateDb2);
     if (rows.length === 0) return null;
     const lastMentioned = /* @__PURE__ */ new Map();
     let maxTime = 0;
@@ -1920,16 +1955,17 @@ function loadRecencyFromStateDb() {
   }
 }
 function saveRecencyToStateDb(index) {
-  if (!moduleStateDb3) {
-    console.error("[Flywheel] saveRecencyToStateDb: No StateDb available (moduleStateDb is null)");
+  const stateDb2 = getStateDb();
+  if (!stateDb2) {
+    console.error("[Flywheel] saveRecencyToStateDb: No StateDb available");
     return;
   }
   console.error(`[Flywheel] saveRecencyToStateDb: Saving ${index.lastMentioned.size} entries...`);
   try {
     for (const [entityNameLower, timestamp] of index.lastMentioned) {
-      recordEntityMention(moduleStateDb3, entityNameLower, new Date(timestamp));
+      recordEntityMention(stateDb2, entityNameLower, new Date(timestamp));
     }
-    const count = moduleStateDb3.db.prepare("SELECT COUNT(*) as cnt FROM recency").get();
+    const count = stateDb2.db.prepare("SELECT COUNT(*) as cnt FROM recency").get();
     console.error(`[Flywheel] Saved recency: ${index.lastMentioned.size} entries \u2192 ${count.cnt} rows in table`);
   } catch (e) {
     console.error("[Flywheel] Failed to save recency to StateDb:", e);
@@ -1939,6 +1975,7 @@ var moduleStateDb3, RECENCY_CACHE_VERSION, EXCLUDED_FOLDERS;
 var init_recency = __esm({
   "src/core/shared/recency.ts"() {
     "use strict";
+    init_vault_scope();
     moduleStateDb3 = null;
     RECENCY_CACHE_VERSION = 1;
     EXCLUDED_FOLDERS = /* @__PURE__ */ new Set([
@@ -2958,6 +2995,114 @@ var init_cooccurrence = __esm({
   }
 });
 
+// src/core/shared/retrievalCooccurrence.ts
+function mineRetrievalCooccurrence(stateDb2) {
+  const db4 = stateDb2.db;
+  const lastRow = db4.prepare(
+    `SELECT value FROM fts_metadata WHERE key = ?`
+  ).get(LAST_PROCESSED_KEY);
+  const lastId = lastRow ? parseInt(lastRow.value, 10) : 0;
+  const toolPlaceholders = Array.from(RETRIEVAL_TOOLS).map(() => "?").join(",");
+  const rows = db4.prepare(`
+    SELECT id, session_id, note_paths, timestamp
+    FROM tool_invocations
+    WHERE id > ? AND tool_name IN (${toolPlaceholders}) AND note_paths IS NOT NULL AND session_id IS NOT NULL
+    ORDER BY id
+  `).all(lastId, ...RETRIEVAL_TOOLS);
+  if (rows.length === 0) return 0;
+  const sessionNotes = /* @__PURE__ */ new Map();
+  for (const row of rows) {
+    let paths;
+    try {
+      paths = JSON.parse(row.note_paths);
+    } catch {
+      continue;
+    }
+    const existing = sessionNotes.get(row.session_id);
+    if (existing) {
+      for (const p of paths) existing.paths.add(p);
+      existing.timestamp = Math.max(existing.timestamp, row.timestamp);
+    } else {
+      sessionNotes.set(row.session_id, {
+        paths: new Set(paths),
+        timestamp: row.timestamp
+      });
+    }
+  }
+  const insertStmt = db4.prepare(`
+    INSERT OR IGNORE INTO retrieval_cooccurrence (note_a, note_b, session_id, timestamp, weight)
+    VALUES (?, ?, ?, ?, ?)
+  `);
+  let inserted = 0;
+  const maxId = rows[rows.length - 1].id;
+  const insertAll = db4.transaction(() => {
+    for (const [sessionId, { paths, timestamp }] of sessionNotes) {
+      const filtered = Array.from(paths).filter((p) => !DAILY_NOTE_RE.test(p));
+      if (filtered.length < 2) continue;
+      const weight = 1 / Math.log(filtered.length);
+      for (let i = 0; i < filtered.length; i++) {
+        for (let j = i + 1; j < filtered.length; j++) {
+          const [a, b] = filtered[i] < filtered[j] ? [filtered[i], filtered[j]] : [filtered[j], filtered[i]];
+          const result = insertStmt.run(a, b, sessionId, timestamp, weight);
+          if (result.changes > 0) inserted++;
+        }
+      }
+    }
+    db4.prepare(
+      `INSERT OR REPLACE INTO fts_metadata (key, value) VALUES (?, ?)`
+    ).run(LAST_PROCESSED_KEY, String(maxId));
+  });
+  insertAll();
+  return inserted;
+}
+function buildRetrievalBoostMap(seedNotePaths, stateDb2) {
+  if (seedNotePaths.size === 0) return /* @__PURE__ */ new Map();
+  const now = Date.now();
+  const halfLifeMs = HALF_LIFE_DAYS * 24 * 60 * 60 * 1e3;
+  const lambda = Math.LN2 / halfLifeMs;
+  const boostMap = /* @__PURE__ */ new Map();
+  for (const seedPath of seedNotePaths) {
+    const rows = stateDb2.db.prepare(`
+      SELECT note_a, note_b, timestamp, weight
+      FROM retrieval_cooccurrence
+      WHERE note_a = ? OR note_b = ?
+    `).all(seedPath, seedPath);
+    for (const row of rows) {
+      const otherNote = row.note_a === seedPath ? row.note_b : row.note_a;
+      if (seedNotePaths.has(otherNote)) continue;
+      const age = now - row.timestamp;
+      const decayFactor = Math.exp(-lambda * age);
+      const w = row.weight * decayFactor;
+      boostMap.set(otherNote, (boostMap.get(otherNote) || 0) + w);
+    }
+  }
+  return boostMap;
+}
+function getRetrievalBoost(entityPath, retrievalBoostMap) {
+  if (!entityPath || retrievalBoostMap.size === 0) return 0;
+  const weight = retrievalBoostMap.get(entityPath) || 0;
+  if (weight <= 0) return 0;
+  return Math.min(Math.round(weight * 3), MAX_RETRIEVAL_BOOST);
+}
+function pruneStaleRetrievalCooccurrence(stateDb2, maxAgeDays = 30) {
+  const cutoff = Date.now() - maxAgeDays * 24 * 60 * 60 * 1e3;
+  const result = stateDb2.db.prepare(
+    "DELETE FROM retrieval_cooccurrence WHERE timestamp < ?"
+  ).run(cutoff);
+  return result.changes;
+}
+var MAX_RETRIEVAL_BOOST, HALF_LIFE_DAYS, LAST_PROCESSED_KEY, DAILY_NOTE_RE, RETRIEVAL_TOOLS;
+var init_retrievalCooccurrence = __esm({
+  "src/core/shared/retrievalCooccurrence.ts"() {
+    "use strict";
+    MAX_RETRIEVAL_BOOST = 6;
+    HALF_LIFE_DAYS = 7;
+    LAST_PROCESSED_KEY = "retrieval_cooc_last_id";
+    DAILY_NOTE_RE = /\d{4}-\d{2}-\d{2}\.md$/;
+    RETRIEVAL_TOOLS = /* @__PURE__ */ new Set(["recall", "search", "search_notes"]);
+  }
+});
+
 // src/core/write/edgeWeights.ts
 function setEdgeWeightStateDb(stateDb2) {
   moduleStateDb4 = stateDb2;
@@ -3179,7 +3324,7 @@ function setWriteStateDb(stateDb2) {
   setRecencyStateDb(stateDb2);
 }
 function getWriteStateDb() {
-  return moduleStateDb5;
+  return getActiveScopeOrNull()?.stateDb ?? moduleStateDb5;
 }
 function setWikilinkConfig(config) {
   moduleConfig = config;
@@ -3713,6 +3858,21 @@ async function suggestRelatedLinks(content, options = {}) {
       if (displayName) cooccurrenceSeeds.add(displayName);
     }
   }
+  const stateDb2 = getWriteStateDb();
+  let retrievalBoostMap = /* @__PURE__ */ new Map();
+  if (!disabled.has("cooccurrence") && stateDb2 && cooccurrenceSeeds.size > 0) {
+    const seedNotePaths = /* @__PURE__ */ new Set();
+    for (const seedName of cooccurrenceSeeds) {
+      const seedEntity = entitiesWithTypes.find((e) => e.entity.name === seedName);
+      if (seedEntity?.entity.path) seedNotePaths.add(seedEntity.entity.path);
+    }
+    if (seedNotePaths.size > 0) {
+      try {
+        retrievalBoostMap = buildRetrievalBoostMap(seedNotePaths, stateDb2);
+      } catch {
+      }
+    }
+  }
   if (!disabled.has("cooccurrence") && cooccurrenceIndex && cooccurrenceSeeds.size > 0) {
     for (const { entity, category } of entitiesWithTypes) {
       const entityName = entity.name;
@@ -3720,7 +3880,9 @@ async function suggestRelatedLinks(content, options = {}) {
       if (!disabled.has("length_filter") && entityName.length > MAX_ENTITY_LENGTH) continue;
       if (!disabled.has("article_filter") && isLikelyArticleTitle(entityName)) continue;
       if (linkedEntities.has(entityName.toLowerCase())) continue;
-      const boost = getCooccurrenceBoost(entityName, cooccurrenceSeeds, cooccurrenceIndex, recencyIndex);
+      const contentCoocBoost = getCooccurrenceBoost(entityName, cooccurrenceSeeds, cooccurrenceIndex, recencyIndex);
+      const retrievalCoocBoost = getRetrievalBoost(entity.path, retrievalBoostMap);
+      const boost = Math.max(contentCoocBoost, retrievalCoocBoost);
       if (boost > 0) {
         const existing = scoredEntities.find((e) => e.name === entityName);
         if (existing) {
@@ -4082,6 +4244,7 @@ var init_wikilinks = __esm({
     init_recency();
     init_stemmer();
     init_cooccurrence();
+    init_retrievalCooccurrence();
     init_recency();
     init_embeddings();
     init_edgeWeights();
@@ -5938,7 +6101,7 @@ var init_taskHelpers = __esm({
 
 // src/index.ts
 import * as path32 from "path";
-import { readFileSync as readFileSync5, realpathSync } from "fs";
+import { readFileSync as readFileSync5, realpathSync, existsSync as existsSync3, statSync as statSync5 } from "fs";
 import { fileURLToPath } from "url";
 import { dirname as dirname6, join as join17 } from "path";
 import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
@@ -7505,6 +7668,7 @@ async function flushLogs() {
 // src/core/read/fts5.ts
 init_vault();
 init_serverLog();
+init_vault_scope();
 import * as fs7 from "fs";
 var EXCLUDED_DIRS3 = /* @__PURE__ */ new Set([
   ".obsidian",
@@ -7526,6 +7690,9 @@ function splitFrontmatter(raw) {
   return { frontmatter: values, body: raw.substring(end + 4) };
 }
 var db2 = null;
+function getDb2() {
+  return getActiveScopeOrNull()?.stateDb?.db ?? db2;
+}
 var state = {
   ready: false,
   building: false,
@@ -7558,10 +7725,11 @@ function shouldIndexFile2(filePath) {
   return !parts.some((part) => EXCLUDED_DIRS3.has(part));
 }
 async function buildFTS5Index(vaultPath2) {
+  const db4 = getDb2();
   try {
     state.error = null;
     state.building = true;
-    if (!db2) {
+    if (!db4) {
       throw new Error("FTS5 database not initialized. Call setFTS5Database() first.");
     }
     const files = await scanVault(vaultPath2);
@@ -7581,16 +7749,16 @@ async function buildFTS5Index(vaultPath2) {
         serverLog("fts5", `Skipping ${file.path}: ${err}`, "warn");
       }
     }
-    const insert = db2.prepare(
+    const insert = db4.prepare(
       "INSERT INTO notes_fts (path, title, frontmatter, content) VALUES (?, ?, ?, ?)"
     );
     const now = /* @__PURE__ */ new Date();
-    const swapAll = db2.transaction(() => {
-      db2.exec("DELETE FROM notes_fts");
+    const swapAll = db4.transaction(() => {
+      db4.exec("DELETE FROM notes_fts");
       for (const row of rows) {
         insert.run(...row);
       }
-      db2.prepare(
+      db4.prepare(
         "INSERT OR REPLACE INTO fts_metadata (key, value) VALUES (?, ?)"
       ).run("last_built", now.toISOString());
     });
@@ -7617,11 +7785,12 @@ async function buildFTS5Index(vaultPath2) {
   }
 }
 function isIndexStale(_vaultPath) {
-  if (!db2) {
+  const db4 = getDb2();
+  if (!db4) {
     return true;
   }
   try {
-    const row = db2.prepare(
+    const row = db4.prepare(
       "SELECT value FROM fts_metadata WHERE key = ?"
     ).get("last_built");
     if (!row) {
@@ -7634,12 +7803,19 @@ function isIndexStale(_vaultPath) {
     return true;
   }
 }
+function sanitizeFTS5Query(query) {
+  if (!query?.trim()) return "";
+  return query.replace(/"/g, '""').replace(/[(){}[\]^~:\-]/g, " ").replace(/\s+/g, " ").trim();
+}
 function searchFTS5(_vaultPath, query, limit = 10) {
-  if (!db2) {
+  const db4 = getDb2();
+  if (!db4) {
     throw new Error("FTS5 database not initialized. Call setFTS5Database() first.");
   }
+  const sanitized = sanitizeFTS5Query(query);
+  if (!sanitized) return [];
   try {
-    const stmt = db2.prepare(`
+    const stmt = db4.prepare(`
       SELECT
         path,
         title,
@@ -7649,11 +7825,11 @@ function searchFTS5(_vaultPath, query, limit = 10) {
       ORDER BY bm25(notes_fts, 0.0, 5.0, 10.0, 1.0)
       LIMIT ?
     `);
-    const results = stmt.all(query, limit);
+    const results = stmt.all(sanitized, limit);
     return results;
   } catch (err) {
-    if (err instanceof Error && err.message.includes("fts5: syntax error")) {
-      throw new Error(`Invalid search query: ${query}. Check FTS5 syntax.`);
+    if (err instanceof Error && err.message.includes("fts5:")) {
+      return [];
     }
     throw err;
   }
@@ -7662,9 +7838,10 @@ function getFTS5State() {
   return { ...state };
 }
 function getContentPreview(notePath, maxChars = 300) {
-  if (!db2) return null;
+  const db4 = getDb2();
+  if (!db4) return null;
   try {
-    const row = db2.prepare(
+    const row = db4.prepare(
       "SELECT substr(content, 1, ?) as preview FROM notes_fts WHERE path = ?"
     ).get(maxChars + 50, notePath);
     if (!row?.preview) return null;
@@ -7675,9 +7852,10 @@ function getContentPreview(notePath, maxChars = 300) {
   }
 }
 function countFTS5Mentions(term) {
-  if (!db2) return 0;
+  const db4 = getDb2();
+  if (!db4) return 0;
   try {
-    const result = db2.prepare(
+    const result = db4.prepare(
       "SELECT COUNT(*) as cnt FROM notes_fts WHERE content MATCH ?"
     ).get(`"${term}"`);
     return result?.cnt ?? 0;
@@ -7828,7 +8006,11 @@ async function getTasksWithDueDates(index, vaultPath2, options = {}) {
 
 // src/core/read/taskCache.ts
 init_serverLog();
+init_vault_scope();
 var db3 = null;
+function getDb3() {
+  return getActiveScopeOrNull()?.stateDb?.db ?? db3;
+}
 var TASK_CACHE_STALE_MS = 30 * 60 * 1e3;
 var cacheReady = false;
 var rebuildInProgress = false;
@@ -7851,7 +8033,8 @@ function isTaskCacheBuilding() {
   return rebuildInProgress;
 }
 async function buildTaskCache(vaultPath2, index, excludeTags) {
-  if (!db3) {
+  const db4 = getDb3();
+  if (!db4) {
     throw new Error("Task cache database not initialized. Call setTaskCacheDatabase() first.");
   }
   if (rebuildInProgress) return;
@@ -7882,16 +8065,16 @@ async function buildTaskCache(vaultPath2, index, excludeTags) {
         ]);
       }
     }
-    const insertStmt = db3.prepare(`
+    const insertStmt = db4.prepare(`
       INSERT OR REPLACE INTO tasks (path, line, text, status, raw, context, tags_json, due_date)
       VALUES (?, ?, ?, ?, ?, ?, ?, ?)
     `);
-    const swapAll = db3.transaction(() => {
-      db3.prepare("DELETE FROM tasks").run();
+    const swapAll = db4.transaction(() => {
+      db4.prepare("DELETE FROM tasks").run();
       for (const row of allRows) {
         insertStmt.run(...row);
       }
-      db3.prepare(
+      db4.prepare(
         "INSERT OR REPLACE INTO fts_metadata (key, value) VALUES (?, ?)"
       ).run("task_cache_built", (/* @__PURE__ */ new Date()).toISOString());
     });
@@ -7904,16 +8087,17 @@ async function buildTaskCache(vaultPath2, index, excludeTags) {
   }
 }
 async function updateTaskCacheForFile(vaultPath2, relativePath) {
-  if (!db3) return;
-  db3.prepare("DELETE FROM tasks WHERE path = ?").run(relativePath);
+  const db4 = getDb3();
+  if (!db4) return;
+  db4.prepare("DELETE FROM tasks WHERE path = ?").run(relativePath);
   const absolutePath = path12.join(vaultPath2, relativePath);
   const tasks = await extractTasksFromNote(relativePath, absolutePath);
   if (tasks.length > 0) {
-    const insertStmt = db3.prepare(`
+    const insertStmt = db4.prepare(`
       INSERT OR REPLACE INTO tasks (path, line, text, status, raw, context, tags_json, due_date)
       VALUES (?, ?, ?, ?, ?, ?, ?, ?)
     `);
-    const insertBatch = db3.transaction(() => {
+    const insertBatch = db4.transaction(() => {
       for (const task of tasks) {
         insertStmt.run(
           task.path,
@@ -7931,11 +8115,13 @@ async function updateTaskCacheForFile(vaultPath2, relativePath) {
   }
 }
 function removeTaskCacheForFile(relativePath) {
-  if (!db3) return;
-  db3.prepare("DELETE FROM tasks WHERE path = ?").run(relativePath);
+  const db4 = getDb3();
+  if (!db4) return;
+  db4.prepare("DELETE FROM tasks WHERE path = ?").run(relativePath);
 }
 function queryTasksFromCache(options) {
-  if (!db3) {
+  const db4 = getDb3();
+  if (!db4) {
     throw new Error("Task cache database not initialized.");
   }
   const { status, folder, tag, excludeTags = [], has_due_date, limit, offset = 0 } = options;
@@ -7974,7 +8160,7 @@ function queryTasksFromCache(options) {
     countParams.push(...excludeTags);
   }
   const countWhere = countConditions.length > 0 ? "WHERE " + countConditions.join(" AND ") : "";
-  const countRows = db3.prepare(
+  const countRows = db4.prepare(
     `SELECT status, COUNT(*) as cnt FROM tasks ${countWhere} GROUP BY status`
   ).all(...countParams);
   let openCount = 0;
@@ -7999,7 +8185,7 @@ function queryTasksFromCache(options) {
     limitClause = " LIMIT ? OFFSET ?";
     queryParams.push(limit, offset);
   }
-  const rows = db3.prepare(
+  const rows = db4.prepare(
     `SELECT path, line, text, status, raw, context, tags_json, due_date FROM tasks ${whereClause} ${orderBy}${limitClause}`
   ).all(...queryParams);
   const tasks = rows.map((row) => ({
@@ -8021,9 +8207,10 @@ function queryTasksFromCache(options) {
   };
 }
 function isTaskCacheStale() {
-  if (!db3) return true;
+  const db4 = getDb3();
+  if (!db4) return true;
   try {
-    const row = db3.prepare(
+    const row = db4.prepare(
       "SELECT value FROM fts_metadata WHERE key = ?"
     ).get("task_cache_built");
     if (!row) return true;
@@ -8372,7 +8559,7 @@ var GetBacklinksOutputSchema = {
   returned_count: z.coerce.number().describe("Number of backlinks returned (may be limited)"),
   backlinks: z.array(BacklinkItemSchema).describe("List of backlinks")
 };
-function registerGraphTools(server2, getIndex, getVaultPath, getStateDb) {
+function registerGraphTools(server2, getIndex, getVaultPath, getStateDb2) {
   server2.registerTool(
     "get_backlinks",
     {
@@ -8503,7 +8690,7 @@ function registerGraphTools(server2, getIndex, getVaultPath, getStateDb) {
       limit: z.number().default(20).describe("Maximum number of results to return")
     },
     async ({ path: notePath, min_weight, limit: requestedLimit }) => {
-      const stateDb2 = getStateDb?.();
+      const stateDb2 = getStateDb2?.();
       if (!stateDb2) {
         return { content: [{ type: "text", text: JSON.stringify({ error: "StateDb not initialized" }) }] };
       }
@@ -8546,7 +8733,7 @@ function registerGraphTools(server2, getIndex, getVaultPath, getStateDb) {
       limit: z.number().default(20).describe("Maximum number of results to return")
     },
     async ({ path: notePath, limit: requestedLimit }) => {
-      const stateDb2 = getStateDb?.();
+      const stateDb2 = getStateDb2?.();
       if (!stateDb2) {
         return { content: [{ type: "text", text: JSON.stringify({ error: "StateDb not initialized" }) }] };
       }
@@ -8667,7 +8854,7 @@ function findEntityMatches(text, entities) {
   }
   return matches.sort((a, b) => a.start - b.start);
 }
-function registerWikilinkTools(server2, getIndex, getVaultPath, getStateDb = () => null) {
+function registerWikilinkTools(server2, getIndex, getVaultPath, getStateDb2 = () => null) {
   const SuggestionSchema = z2.object({
     entity: z2.string().describe("The matched text in the input"),
     start: z2.coerce.number().describe("Start position in text (0-indexed)"),
@@ -8809,7 +8996,7 @@ function registerWikilinkTools(server2, getIndex, getVaultPath, getStateDb = ()
           strictness: "balanced"
         });
         if (scored.detailed) {
-          const stateDb2 = getStateDb();
+          const stateDb2 = getStateDb2();
           if (stateDb2) {
             try {
               const weightedStats = getWeightedEntityStats(stateDb2);
@@ -9600,7 +9787,7 @@ function getSweepResults() {
 init_wikilinkFeedback();
 init_embeddings();
 var STALE_THRESHOLD_SECONDS = 300;
-function registerHealthTools(server2, getIndex, getVaultPath, getConfig2 = () => ({}), getStateDb = () => null, getWatcherStatus2 = () => null) {
+function registerHealthTools(server2, getIndex, getVaultPath, getConfig2 = () => ({}), getStateDb2 = () => null, getWatcherStatus2 = () => null) {
   const IndexProgressSchema = z3.object({
     parsed: z3.coerce.number().describe("Number of files parsed so far"),
     total: z3.coerce.number().describe("Total number of files to parse")
@@ -9721,6 +9908,21 @@ function registerHealthTools(server2, getIndex, getVaultPath, getConfig2 = () =>
         vaultAccessible = false;
         recommendations.push("Vault path is not accessible. Check PROJECT_PATH environment variable.");
       }
+      let dbIntegrityFailed = false;
+      const stateDb2 = getStateDb2();
+      if (stateDb2) {
+        try {
+          const result = stateDb2.db.pragma("quick_check");
+          const ok = result.length === 1 && Object.values(result[0])[0] === "ok";
+          if (!ok) {
+            dbIntegrityFailed = true;
+            recommendations.push(`Database integrity check failed: ${Object.values(result[0])[0] ?? "unknown error"}`);
+          }
+        } catch (err) {
+          dbIntegrityFailed = true;
+          recommendations.push(`Database integrity check error: ${err instanceof Error ? err.message : err}`);
+        }
+      }
       const indexBuilt = indexState2 === "ready" && index !== void 0 && index.notes !== void 0;
       const indexAge = indexBuilt && index.builtAt ? Math.floor((Date.now() - index.builtAt.getTime()) / 1e3) : -1;
       const indexStale = indexBuilt && indexAge > STALE_THRESHOLD_SECONDS;
@@ -9744,7 +9946,7 @@ function registerHealthTools(server2, getIndex, getVaultPath, getConfig2 = () =>
         recommendations.push("No notes found in vault. Is PROJECT_PATH pointing to a markdown vault?");
       }
       let status;
-      if (!vaultAccessible || indexState2 === "error") {
+      if (!vaultAccessible || indexState2 === "error" || dbIntegrityFailed) {
         status = "unhealthy";
       } else if (indexState2 === "building" || indexStale || recommendations.length > 0) {
         status = "degraded";
@@ -9769,7 +9971,6 @@ function registerHealthTools(server2, getIndex, getVaultPath, getConfig2 = () =>
       const config = getConfig2();
       const configInfo = Object.keys(config).length > 0 ? config : void 0;
       let lastRebuild;
-      const stateDb2 = getStateDb();
       if (stateDb2) {
         try {
           const events = getRecentIndexEvents(stateDb2, 1);
@@ -10071,7 +10272,7 @@ function registerHealthTools(server2, getIndex, getVaultPath, getConfig2 = () =>
       const checks = [];
       const index = getIndex();
       const vaultPath2 = getVaultPath();
-      const stateDb2 = getStateDb();
+      const stateDb2 = getStateDb2();
       const watcherStatus = getWatcherStatus2();
       checks.push({
         name: "schema_version",
@@ -10517,6 +10718,7 @@ function enrichNoteResult(notePath, stateDb2, index) {
 }
 
 // src/tools/read/query.ts
+init_wikilinkFeedback();
 function matchesFrontmatter(note, where) {
   for (const [key, value] of Object.entries(where)) {
     const noteValue = note.frontmatter[key];
@@ -10584,7 +10786,7 @@ function sortNotes(notes, sortBy, order) {
   });
   return sorted;
 }
-function registerQueryTools(server2, getIndex, getVaultPath, getStateDb) {
+function registerQueryTools(server2, getIndex, getVaultPath, getStateDb2) {
   server2.tool(
     "search",
     'Search the vault \u2014 always start with just a query, no filters. Top results get full metadata (frontmatter, top backlinks/outlinks ranked by edge weight + recency); remaining results get lightweight summaries. Narrow with filters only if the broad search returns too many irrelevant results. Use get_note_structure for headings/full structure, get_backlinks for complete backlink lists.\n\nSearches across content (FTS5 full-text + hybrid semantic), entities (people/projects/technologies), and metadata (frontmatter/tags/folders). Hybrid semantic results are automatically included when embeddings have been built (via init_semantic).\n\nExample: search({ query: "quarterly review", limit: 5 })\nExample: search({ where: { type: "project", status: "active" } })\n\nMulti-vault: when configured with multiple vaults, omitting the `vault` parameter searches all vaults and merges results (each result includes a `vault` field). Pass `vault` to search a specific vault.',
@@ -10618,7 +10820,7 @@ function registerQueryTools(server2, getIndex, getVaultPath, getStateDb) {
       const index = getIndex();
       const vaultPath2 = getVaultPath();
       if (prefix && query) {
-        const stateDb2 = getStateDb();
+        const stateDb2 = getStateDb2();
         if (!stateDb2) {
           return { content: [{ type: "text", text: JSON.stringify({ results: [], count: 0, query, error: "StateDb not initialized" }, null, 2) }] };
         }
@@ -10666,7 +10868,7 @@ function registerQueryTools(server2, getIndex, getVaultPath, getStateDb) {
         matchingNotes = sortNotes(matchingNotes, sort_by ?? "modified", order ?? "desc");
         const totalMatches = matchingNotes.length;
         const limitedNotes = matchingNotes.slice(0, limit);
-        const stateDb2 = getStateDb();
+        const stateDb2 = getStateDb2();
         const notes = limitedNotes.map(
           (note, i) => (i < detailN ? enrichResult : enrichResultLight)({ path: note.path, title: note.title }, index, stateDb2)
         );
@@ -10694,7 +10896,7 @@ function registerQueryTools(server2, getIndex, getVaultPath, getStateDb) {
         }
         const fts5Results = searchFTS5(vaultPath2, query, limit);
         let entityResults = [];
-        const stateDbEntity = getStateDb();
+        const stateDbEntity = getStateDb2();
         if (stateDbEntity) {
           try {
             entityResults = searchEntities(stateDbEntity, query, limit);
@@ -10703,7 +10905,7 @@ function registerQueryTools(server2, getIndex, getVaultPath, getStateDb) {
         }
         let edgeRanked = [];
         if (context_note) {
-          const ctxStateDb = getStateDb();
+          const ctxStateDb = getStateDb2();
           if (ctxStateDb) {
             try {
               const edgeRows = ctxStateDb.db.prepare(`
@@ -10768,7 +10970,7 @@ function registerQueryTools(server2, getIndex, getVaultPath, getStateDb) {
             }));
             scored.sort((a, b) => b.rrf_score - a.rrf_score);
             const filtered = applyFolderFilter(scored);
-            const stateDb2 = getStateDb();
+            const stateDb2 = getStateDb2();
             const results = filtered.slice(0, limit).map((item, i) => ({
               ...(i < detailN ? enrichResult : enrichResultLight)({ path: item.path, title: item.title, snippet: item.snippet }, index, stateDb2),
               rrf_score: item.rrf_score,
@@ -10776,6 +10978,34 @@ function registerQueryTools(server2, getIndex, getVaultPath, getStateDb) {
               in_semantic: item.in_semantic,
               in_entity: item.in_entity
             }));
+            if (stateDb2 && results.length < limit) {
+              const existingPaths = new Set(results.map((r) => r.path));
+              const backfill = [];
+              for (const r of results.slice(0, 3)) {
+                const rPath = r.path;
+                if (!rPath) continue;
+                try {
+                  const outlinks = getStoredNoteLinks(stateDb2, rPath);
+                  for (const target of outlinks) {
+                    const entityRow = stateDb2.db.prepare(
+                      "SELECT path FROM entities WHERE name_lower = ?"
+                    ).get(target);
+                    if (entityRow?.path && !existingPaths.has(entityRow.path)) {
+                      existingPaths.add(entityRow.path);
+                      backfill.push({
+                        ...enrichResultLight({ path: entityRow.path, title: target }, index, stateDb2),
+                        rrf_score: 0,
+                        in_fts5: false,
+                        in_semantic: false,
+                        in_entity: false
+                      });
+                    }
+                  }
+                } catch {
+                }
+              }
+              results.push(...backfill.slice(0, limit - results.length));
+            }
             return { content: [{ type: "text", text: JSON.stringify({
               method: "hybrid",
               query,
@@ -10795,12 +11025,36 @@ function registerQueryTools(server2, getIndex, getVaultPath, getStateDb) {
             ...entityRanked.map((r) => ({ path: r.path, title: r.name, snippet: void 0, in_entity: true }))
           ];
           const filtered = applyFolderFilter(mergedItems);
-          const stateDb2 = getStateDb();
+          const stateDb2 = getStateDb2();
           const sliced = filtered.slice(0, limit);
           const results = sliced.map((item, i) => ({
             ...(i < detailN ? enrichResult : enrichResultLight)({ path: item.path, title: item.title, snippet: item.snippet }, index, stateDb2),
             ..."in_fts5" in item ? { in_fts5: true } : { in_entity: true }
           }));
+          if (stateDb2 && results.length < limit) {
+            const existingPaths = new Set(results.map((r) => r.path));
+            const backfill = [];
+            for (const r of results.slice(0, 3)) {
+              const rPath = r.path;
+              if (!rPath) continue;
+              try {
+                const outlinks = getStoredNoteLinks(stateDb2, rPath);
+                for (const target of outlinks) {
+                  const entityRow = stateDb2.db.prepare(
+                    "SELECT path FROM entities WHERE name_lower = ?"
+                  ).get(target);
+                  if (entityRow?.path && !existingPaths.has(entityRow.path)) {
+                    existingPaths.add(entityRow.path);
+                    backfill.push({
+                      ...enrichResultLight({ path: entityRow.path, title: target }, index, stateDb2)
+                    });
+                  }
+                }
+              } catch {
+              }
+            }
+            results.push(...backfill.slice(0, limit - results.length));
+          }
           return { content: [{ type: "text", text: JSON.stringify({
             method: "fts5",
             query,
@@ -10808,7 +11062,7 @@ function registerQueryTools(server2, getIndex, getVaultPath, getStateDb) {
             results
           }, null, 2) }] };
         }
-        const stateDbFts = getStateDb();
+        const stateDbFts = getStateDb2();
         const fts5Filtered = applyFolderFilter(fts5Results);
         const enrichedFts5 = fts5Filtered.map((r, i) => ({ ...(i < detailN ? enrichResult : enrichResultLight)({ path: r.path, title: r.title, snippet: r.snippet }, index, stateDbFts), in_fts5: true }));
         return { content: [{ type: "text", text: JSON.stringify({
@@ -10896,7 +11150,7 @@ function suggestEntityAliases(stateDb2, folder) {
 
 // src/tools/read/system.ts
 init_edgeWeights();
-function registerSystemTools(server2, getIndex, setIndex, getVaultPath, setConfig, getStateDb) {
+function registerSystemTools(server2, getIndex, setIndex, getVaultPath, setConfig, getStateDb2) {
   const RefreshIndexOutputSchema = {
     success: z5.boolean().describe("Whether the refresh succeeded"),
     notes_count: z5.number().describe("Number of notes indexed"),
@@ -10922,7 +11176,7 @@ function registerSystemTools(server2, getIndex, setIndex, getVaultPath, setConfi
         const newIndex = await buildVaultIndex(vaultPath2);
         setIndex(newIndex);
         setIndexState("ready");
-        const stateDb2 = getStateDb?.();
+        const stateDb2 = getStateDb2?.();
         if (stateDb2) {
           try {
             const entityIndex2 = await scanVaultEntities2(vaultPath2, {
@@ -11009,7 +11263,7 @@ function registerSystemTools(server2, getIndex, setIndex, getVaultPath, setConfi
         setIndexState("error");
         setIndexError(err instanceof Error ? err : new Error(String(err)));
         const duration = Date.now() - startTime;
-        const stateDb2 = getStateDb?.();
+        const stateDb2 = getStateDb2?.();
         if (stateDb2) {
           recordIndexEvent(stateDb2, {
             trigger: "manual_refresh",
@@ -11267,7 +11521,7 @@ function registerSystemTools(server2, getIndex, setIndex, getVaultPath, setConfi
       category,
       limit: perCategoryLimit
     }) => {
-      const stateDb2 = getStateDb?.();
+      const stateDb2 = getStateDb2?.();
       if (!stateDb2) {
         return {
           content: [{ type: "text", text: JSON.stringify({ error: "StateDb not available" }) }]
@@ -11322,7 +11576,7 @@ function registerSystemTools(server2, getIndex, setIndex, getVaultPath, setConfi
       folder,
       limit: requestedLimit
     }) => {
-      const stateDb2 = getStateDb?.();
+      const stateDb2 = getStateDb2?.();
       if (!stateDb2) {
         return {
           content: [{ type: "text", text: JSON.stringify({ error: "StateDb not available" }) }]
@@ -11542,7 +11796,7 @@ async function findSections(index, headingPattern, vaultPath2, folder) {
 
 // src/tools/read/primitives.ts
 import { getEntityByName as getEntityByName3 } from "@velvetmonkey/vault-core";
-function registerPrimitiveTools(server2, getIndex, getVaultPath, getConfig2 = () => ({}), getStateDb = () => null) {
+function registerPrimitiveTools(server2, getIndex, getVaultPath, getConfig2 = () => ({}), getStateDb2 = () => null) {
   server2.registerTool(
     "get_note_structure",
     {
@@ -11581,7 +11835,7 @@ function registerPrimitiveTools(server2, getIndex, getVaultPath, getConfig2 = ()
         enriched.backlink_count = backlinks.length;
         enriched.outlink_count = note.outlinks.length;
       }
-      const stateDb2 = getStateDb();
+      const stateDb2 = getStateDb2();
       if (stateDb2 && note) {
         try {
           const entity = getEntityByName3(stateDb2, note.title);
@@ -12640,7 +12894,7 @@ function getExcludedPaths(index, config) {
   }
   return excluded;
 }
-function registerGraphAnalysisTools(server2, getIndex, getVaultPath, getStateDb, getConfig2) {
+function registerGraphAnalysisTools(server2, getIndex, getVaultPath, getStateDb2, getConfig2) {
   server2.registerTool(
     "graph_analysis",
     {
@@ -12810,7 +13064,7 @@ function registerGraphAnalysisTools(server2, getIndex, getVaultPath, getStateDb,
           };
         }
         case "emerging_hubs": {
-          const db4 = getStateDb?.();
+          const db4 = getStateDb2?.();
           if (!db4) {
             return {
               content: [{ type: "text", text: JSON.stringify({
@@ -17558,7 +17812,7 @@ function registerTagTools(server2, getIndex, getVaultPath) {
 // src/tools/write/wikilinkFeedback.ts
 init_wikilinkFeedback();
 import { z as z22 } from "zod";
-function registerWikilinkFeedbackTools(server2, getStateDb) {
+function registerWikilinkFeedbackTools(server2, getStateDb2) {
   server2.registerTool(
     "wikilink_feedback",
     {
@@ -17579,7 +17833,7 @@ function registerWikilinkFeedbackTools(server2, getStateDb) {
       }
     },
     async ({ mode, entity, note_path, context, correct, limit, days_back, granularity, timestamp_before, timestamp_after, skip_status_update }) => {
-      const stateDb2 = getStateDb();
+      const stateDb2 = getStateDb2();
       if (!stateDb2) {
         return {
           content: [{ type: "text", text: JSON.stringify({ error: "StateDb not available \u2014 database not initialized yet" }) }],
@@ -17741,7 +17995,7 @@ function registerWikilinkFeedbackTools(server2, getStateDb) {
 // src/tools/write/corrections.ts
 init_corrections();
 import { z as z23 } from "zod";
-function registerCorrectionTools(server2, getStateDb) {
+function registerCorrectionTools(server2, getStateDb2) {
   server2.tool(
     "vault_record_correction",
     'Record a persistent correction (e.g., "that link is wrong", "undo that"). Survives across sessions.',
@@ -17752,7 +18006,7 @@ function registerCorrectionTools(server2, getStateDb) {
       note_path: z23.string().optional().describe("Note path (if correction is about a specific note)")
     },
     async ({ correction_type, description, entity, note_path }) => {
-      const stateDb2 = getStateDb();
+      const stateDb2 = getStateDb2();
       if (!stateDb2) {
         return {
           content: [{ type: "text", text: JSON.stringify({ error: "StateDb not available" }) }],
@@ -17780,7 +18034,7 @@ function registerCorrectionTools(server2, getStateDb) {
       limit: z23.number().min(1).max(200).default(50).describe("Max entries to return")
     },
     async ({ status, entity, limit }) => {
-      const stateDb2 = getStateDb();
+      const stateDb2 = getStateDb2();
       if (!stateDb2) {
         return {
           content: [{ type: "text", text: JSON.stringify({ error: "StateDb not available" }) }],
@@ -17807,7 +18061,7 @@ function registerCorrectionTools(server2, getStateDb) {
       status: z23.enum(["applied", "dismissed"]).describe("New status")
     },
     async ({ correction_id, status }) => {
-      const stateDb2 = getStateDb();
+      const stateDb2 = getStateDb2();
       if (!stateDb2) {
         return {
           content: [{ type: "text", text: JSON.stringify({ error: "StateDb not available" }) }],
@@ -18155,7 +18409,7 @@ function findContradictions2(stateDb2, entity) {
 }
 
 // src/tools/write/memory.ts
-function registerMemoryTools(server2, getStateDb) {
+function registerMemoryTools(server2, getStateDb2) {
   server2.tool(
     "memory",
     "Store, retrieve, search, and manage agent working memory. Actions: store, get, search, list, forget, summarize_session.",
@@ -18180,7 +18434,7 @@ function registerMemoryTools(server2, getStateDb) {
       tool_count: z24.number().optional().describe("Number of tool calls in session")
     },
     async (args) => {
-      const stateDb2 = getStateDb();
+      const stateDb2 = getStateDb2();
       if (!stateDb2) {
         return {
           content: [{ type: "text", text: JSON.stringify({ error: "StateDb not available" }) }],
@@ -18771,7 +19025,7 @@ async function performRecall(stateDb2, query, options = {}) {
   }
   return selected;
 }
-function registerRecallTools(server2, getStateDb, getVaultPath, getIndex) {
+function registerRecallTools(server2, getStateDb2, getVaultPath, getIndex) {
   server2.tool(
     "recall",
     "Query everything the system knows about a topic. Searches across entities, notes, and memories with graph-boosted ranking.",
@@ -18784,7 +19038,7 @@ function registerRecallTools(server2, getStateDb, getVaultPath, getIndex) {
       diversity: z25.number().min(0).max(1).optional().describe("Relevance vs diversity tradeoff (0=max diversity, 1=pure relevance, default: 0.7)")
     },
     async (args) => {
-      const stateDb2 = getStateDb();
+      const stateDb2 = getStateDb2();
       if (!stateDb2) {
         return {
           content: [{ type: "text", text: JSON.stringify({ error: "StateDb not available" }) }],
@@ -18840,15 +19094,17 @@ import { z as z26 } from "zod";
 // src/core/shared/toolTracking.ts
 function recordToolInvocation(stateDb2, event) {
   stateDb2.db.prepare(
-    `INSERT INTO tool_invocations (timestamp, tool_name, session_id, note_paths, duration_ms, success)
-     VALUES (?, ?, ?, ?, ?, ?)`
+    `INSERT INTO tool_invocations (timestamp, tool_name, session_id, note_paths, duration_ms, success, response_tokens, baseline_tokens)
+     VALUES (?, ?, ?, ?, ?, ?, ?, ?)`
   ).run(
     Date.now(),
     event.tool_name,
     event.session_id ?? null,
     event.note_paths ? JSON.stringify(event.note_paths) : null,
     event.duration_ms ?? null,
-    event.success !== false ? 1 : 0
+    event.success !== false ? 1 : 0,
+    event.response_tokens ?? null,
+    event.baseline_tokens ?? null
   );
 }
 function rowToInvocation(row) {
@@ -18859,7 +19115,9 @@ function rowToInvocation(row) {
     session_id: row.session_id,
     note_paths: row.note_paths ? JSON.parse(row.note_paths) : null,
     duration_ms: row.duration_ms,
-    success: row.success === 1
+    success: row.success === 1,
+    response_tokens: row.response_tokens,
+    baseline_tokens: row.baseline_tokens
   };
 }
 function getToolUsageSummary(stateDb2, daysBack = 30) {
@@ -19119,7 +19377,7 @@ function buildVaultPulseSection(stateDb2) {
     estimated_tokens: estimateTokens2(content)
   };
 }
-function registerBriefTools(server2, getStateDb) {
+function registerBriefTools(server2, getStateDb2) {
   server2.tool(
     "brief",
     "Get a startup context briefing: recent sessions, active entities, memories, pending corrections, and vault stats. Call at conversation start.",
@@ -19128,7 +19386,7 @@ function registerBriefTools(server2, getStateDb) {
       focus: z26.string().optional().describe("Focus entity or topic (filters content)")
     },
     async (args) => {
-      const stateDb2 = getStateDb();
+      const stateDb2 = getStateDb2();
       if (!stateDb2) {
         return {
           content: [{ type: "text", text: JSON.stringify({ error: "StateDb not available" }) }],
@@ -19189,7 +19447,7 @@ var VALID_CONFIG_KEYS = {
   implicit_patterns: z27.array(z27.string()),
   adaptive_strictness: z27.boolean()
 };
-function registerConfigTools(server2, getConfig2, setConfig, getStateDb) {
+function registerConfigTools(server2, getConfig2, setConfig, getStateDb2) {
   server2.registerTool(
     "flywheel_config",
     {
@@ -19231,7 +19489,7 @@ function registerConfigTools(server2, getConfig2, setConfig, getStateDb) {
               }) }]
             };
           }
-          const stateDb2 = getStateDb();
+          const stateDb2 = getStateDb2();
           if (!stateDb2) {
             return {
               content: [{ type: "text", text: JSON.stringify({ error: "StateDb not available" }) }]
@@ -19553,7 +19811,7 @@ async function executeEnrich(stateDb2, vaultPath2, dryRun, batchSize, offset) {
     total_enriched: currentTotal
   };
 }
-function registerInitTools(server2, getVaultPath, getStateDb) {
+function registerInitTools(server2, getVaultPath, getStateDb2) {
   server2.tool(
     "vault_init",
     `Initialize vault for Flywheel. Modes: "status" (check what's ready/missing), "run" (execute missing init steps), "enrich" (scan notes with zero wikilinks and apply entity links).`,
@@ -19564,7 +19822,7 @@ function registerInitTools(server2, getVaultPath, getStateDb) {
       offset: z28.number().default(0).describe("For enrich mode: skip this many eligible notes (for pagination)")
     },
     async ({ mode, dry_run, batch_size, offset }) => {
-      const stateDb2 = getStateDb();
+      const stateDb2 = getStateDb2();
       const vaultPath2 = getVaultPath();
       switch (mode) {
         case "status": {
@@ -19748,7 +20006,7 @@ function purgeOldMetrics(stateDb2, retentionDays = 90) {
 }
 
 // src/tools/read/metrics.ts
-function registerMetricsTools(server2, getIndex, getStateDb) {
+function registerMetricsTools(server2, getIndex, getStateDb2) {
   server2.registerTool(
     "vault_growth",
     {
@@ -19763,7 +20021,7 @@ function registerMetricsTools(server2, getIndex, getStateDb) {
     },
     async ({ mode, metric, days_back, limit: eventLimit }) => {
       const index = getIndex();
-      const stateDb2 = getStateDb();
+      const stateDb2 = getStateDb2();
       const daysBack = days_back ?? 30;
       let result;
       switch (mode) {
@@ -19832,7 +20090,7 @@ function registerMetricsTools(server2, getIndex, getStateDb) {
 
 // src/tools/read/activity.ts
 import { z as z30 } from "zod";
-function registerActivityTools(server2, getStateDb, getSessionId2) {
+function registerActivityTools(server2, getStateDb2, getSessionId2) {
   server2.registerTool(
     "vault_activity",
     {
@@ -19846,7 +20104,7 @@ function registerActivityTools(server2, getStateDb, getSessionId2) {
       }
     },
     async ({ mode, session_id, days_back, limit: resultLimit }) => {
-      const stateDb2 = getStateDb();
+      const stateDb2 = getStateDb2();
       if (!stateDb2) {
         return {
           content: [{ type: "text", text: JSON.stringify({ error: "StateDb not available" }) }]
@@ -20181,7 +20439,7 @@ async function findHybridSimilarNotes(db4, vaultPath2, index, sourcePath, option
 
 // src/tools/read/similarity.ts
 init_embeddings();
-function registerSimilarityTools(server2, getIndex, getVaultPath, getStateDb) {
+function registerSimilarityTools(server2, getIndex, getVaultPath, getStateDb2) {
   server2.registerTool(
     "find_similar",
     {
@@ -20196,7 +20454,7 @@ function registerSimilarityTools(server2, getIndex, getVaultPath, getStateDb) {
     async ({ path: path33, limit, diversity }) => {
       const index = getIndex();
       const vaultPath2 = getVaultPath();
-      const stateDb2 = getStateDb();
+      const stateDb2 = getStateDb2();
       if (!stateDb2) {
         return {
           content: [{ type: "text", text: JSON.stringify({ error: "StateDb not available" }) }]
@@ -20237,7 +20495,7 @@ function registerSimilarityTools(server2, getIndex, getVaultPath, getStateDb) {
 init_embeddings();
 import { z as z32 } from "zod";
 import { getAllEntitiesFromDb } from "@velvetmonkey/vault-core";
-function registerSemanticTools(server2, getVaultPath, getStateDb) {
+function registerSemanticTools(server2, getVaultPath, getStateDb2) {
   server2.registerTool(
     "init_semantic",
     {
@@ -20250,7 +20508,7 @@ function registerSemanticTools(server2, getVaultPath, getStateDb) {
       }
     },
     async ({ force }) => {
-      const stateDb2 = getStateDb();
+      const stateDb2 = getStateDb2();
       if (!stateDb2) {
         return {
           content: [{
@@ -20344,7 +20602,7 @@ import { getAllEntitiesFromDb as getAllEntitiesFromDb2, getDismissedMergePairs,
 function normalizeName(name) {
   return name.toLowerCase().replace(/[.\-_]/g, "").replace(/js$/, "").replace(/ts$/, "");
 }
-function registerMergeTools2(server2, getStateDb) {
+function registerMergeTools2(server2, getStateDb2) {
   server2.tool(
     "suggest_entity_merges",
     "Find potential duplicate entities that could be merged based on name similarity",
@@ -20352,7 +20610,7 @@ function registerMergeTools2(server2, getStateDb) {
       limit: z33.number().optional().default(50).describe("Maximum number of suggestions to return")
     },
     async ({ limit }) => {
-      const stateDb2 = getStateDb();
+      const stateDb2 = getStateDb2();
       if (!stateDb2) {
         return {
           content: [{ type: "text", text: JSON.stringify({ suggestions: [], error: "StateDb not available" }) }]
@@ -20458,7 +20716,7 @@ function registerMergeTools2(server2, getStateDb) {
       reason: z33.string().describe("Original suggestion reason")
     },
     async ({ source_path, target_path, source_name, target_name, reason }) => {
-      const stateDb2 = getStateDb();
+      const stateDb2 = getStateDb2();
       if (!stateDb2) {
         return {
           content: [{ type: "text", text: JSON.stringify({ dismissed: false, error: "StateDb not available" }) }]
@@ -20993,7 +21251,7 @@ function handleTemporalSummary(index, stateDb2, startDate, endDate, focusEntitie
     content: [{ type: "text", text: JSON.stringify(output, null, 2) }]
   };
 }
-function registerTemporalAnalysisTools(server2, getIndex, getVaultPath, getStateDb) {
+function registerTemporalAnalysisTools(server2, getIndex, getVaultPath, getStateDb2) {
   server2.registerTool(
     "get_context_around_date",
     {
@@ -21008,7 +21266,7 @@ function registerTemporalAnalysisTools(server2, getIndex, getVaultPath, getState
     async ({ date, window_days, limit: requestedLimit }) => {
       requireIndex();
       const limit = Math.min(requestedLimit ?? 50, MAX_LIMIT);
-      return handleGetContextAroundDate(getIndex(), getStateDb(), date, window_days ?? 3, limit);
+      return handleGetContextAroundDate(getIndex(), getStateDb2(), date, window_days ?? 3, limit);
     }
   );
   server2.registerTool(
@@ -21030,7 +21288,7 @@ function registerTemporalAnalysisTools(server2, getIndex, getVaultPath, getState
       const limit = Math.min(requestedLimit ?? 30, MAX_LIMIT);
       return handlePredictStaleNotes(
         getIndex(),
-        getStateDb(),
+        getStateDb2(),
         days ?? 30,
         min_importance ?? 0,
         include_recommendations ?? true,
@@ -21055,7 +21313,7 @@ function registerTemporalAnalysisTools(server2, getIndex, getVaultPath, getState
       requireIndex();
       return handleTrackConceptEvolution(
         getIndex(),
-        getStateDb(),
+        getStateDb2(),
         entity,
         days_back ?? 90,
         include_cooccurrence ?? true
@@ -21079,7 +21337,7 @@ function registerTemporalAnalysisTools(server2, getIndex, getVaultPath, getState
       const limit = Math.min(requestedLimit ?? 50, MAX_LIMIT);
       return handleTemporalSummary(
         getIndex(),
-        getStateDb(),
+        getStateDb2(),
         start_date,
         end_date,
         focus_entities,
@@ -21094,6 +21352,7 @@ init_serverLog();
 init_wikilinkFeedback();
 init_recency();
 init_cooccurrence();
+init_retrievalCooccurrence();
 init_corrections();
 init_edgeWeights();
 import * as fs32 from "node:fs/promises";
@@ -21244,10 +21503,14 @@ function parseVaultConfig() {
   for (const entry of envValue.split(",")) {
     const trimmed = entry.trim();
     const colonIdx = trimmed.indexOf(":");
-    if (colonIdx <= 0) continue;
+    if (colonIdx <= 0) {
+      console.error(`[flywheel] Warning: skipping malformed FLYWHEEL_VAULTS entry: "${trimmed}" (expected name:/path)`);
+      continue;
+    }
     let name;
     let vaultPath2;
     if (colonIdx === 1 && trimmed.length > 2 && (trimmed[2] === "\\" || trimmed[2] === "/")) {
+      console.error(`[flywheel] Warning: skipping ambiguous FLYWHEEL_VAULTS entry: "${trimmed}" (looks like a Windows path, not name:path)`);
       continue;
     }
     name = trimmed.substring(0, colonIdx);
@@ -21271,6 +21534,11 @@ try {
 } catch {
   resolvedVaultPath = vaultPath.replace(/\\/g, "/");
 }
+if (!existsSync3(resolvedVaultPath)) {
+  console.error(`[flywheel] Fatal: vault path does not exist: ${resolvedVaultPath}`);
+  console.error(`[flywheel] Set PROJECT_PATH or VAULT_PATH to a valid Obsidian vault directory.`);
+  process.exit(1);
+}
 var vaultIndex;
 var flywheelConfig = {};
 var stateDb = null;
@@ -21574,7 +21842,7 @@ Use "note_intelligence" for per-note analysis (completeness, quality, suggestion
   }
   return parts.join("\n");
 }
-function applyToolGating(targetServer, categories, getDb, registry) {
+function applyToolGating(targetServer, categories, getDb4, registry, getVaultPath) {
   let _registered = 0;
   let _skipped = 0;
   function gate(name) {
@@ -21591,6 +21859,7 @@ function applyToolGating(targetServer, categories, getDb, registry) {
       const start = Date.now();
       let success = true;
       let notePaths;
+      let result;
       const params = args[0];
       if (params && typeof params === "object") {
         const paths = [];
@@ -21602,12 +21871,13 @@ function applyToolGating(targetServer, categories, getDb, registry) {
         if (paths.length > 0) notePaths = paths;
       }
       try {
-        return await handler(...args);
+        result = await handler(...args);
+        return result;
       } catch (err) {
         success = false;
         throw err;
       } finally {
-        const db4 = getDb();
+        const db4 = getDb4();
         if (db4) {
           try {
             let sessionId;
@@ -21615,12 +21885,36 @@ function applyToolGating(targetServer, categories, getDb, registry) {
               sessionId = getSessionId();
             } catch {
             }
+            let responseTokens;
+            if (result?.content) {
+              let totalChars = 0;
+              for (const block of result.content) {
+                if (block?.type === "text" && typeof block.text === "string") {
+                  totalChars += block.text.length;
+                }
+              }
+              if (totalChars > 0) responseTokens = Math.ceil(totalChars / 4);
+            }
+            let baselineTokens;
+            if (notePaths && notePaths.length > 0 && getVaultPath) {
+              const vp = getVaultPath();
+              let totalBytes = 0;
+              for (const p of notePaths) {
+                try {
+                  totalBytes += statSync5(path32.join(vp, p)).size;
+                } catch {
+                }
+              }
+              if (totalBytes > 0) baselineTokens = Math.ceil(totalBytes / 4);
+            }
             recordToolInvocation(db4, {
               tool_name: toolName,
               session_id: sessionId,
               note_paths: notePaths,
               duration_ms: Date.now() - start,
-              success
+              success,
+              response_tokens: responseTokens,
+              baseline_tokens: baselineTokens
             });
           } catch {
           }
@@ -21642,21 +21936,15 @@ function applyToolGating(targetServer, categories, getDb, registry) {
       }
       const ctx = registry.getContext(vaultName);
       activateVault(ctx);
-      stateDb = ctx.stateDb;
-      vaultIndex = ctx.vaultIndex;
-      flywheelConfig = ctx.flywheelConfig;
-      return handler(...args);
+      return runInVaultScope(buildVaultScope(ctx), () => handler(...args));
     };
   }
   async function crossVaultSearch(reg, handler, args) {
     const perVault = [];
     for (const ctx of reg.getAllContexts()) {
       activateVault(ctx);
-      stateDb = ctx.stateDb;
-      vaultIndex = ctx.vaultIndex;
-      flywheelConfig = ctx.flywheelConfig;
       try {
-        const result = await handler(...args);
+        const result = await runInVaultScope(buildVaultScope(ctx), () => handler(...args));
         const text = result?.content?.[0]?.text;
         if (text) {
           perVault.push({ vault: ctx.name, data: JSON.parse(text) });
@@ -21738,39 +22026,43 @@ function applyToolGating(targetServer, categories, getDb, registry) {
   } };
 }
 function registerAllTools(targetServer) {
-  registerHealthTools(targetServer, () => vaultIndex, () => vaultPath, () => flywheelConfig, () => stateDb, getWatcherStatus);
+  const gvp = () => getActiveScopeOrNull()?.vaultPath ?? vaultPath;
+  const gvi = () => getActiveScopeOrNull()?.vaultIndex ?? vaultIndex;
+  const gsd = () => getActiveScopeOrNull()?.stateDb ?? stateDb;
+  const gcf = () => getActiveScopeOrNull()?.flywheelConfig ?? flywheelConfig;
+  registerHealthTools(targetServer, gvi, gvp, gcf, gsd, getWatcherStatus);
   registerSystemTools(
     targetServer,
-    () => vaultIndex,
+    gvi,
     (newIndex) => {
       vaultIndex = newIndex;
     },
-    () => vaultPath,
+    gvp,
     (newConfig) => {
       flywheelConfig = newConfig;
       setWikilinkConfig(newConfig);
     },
-    () => stateDb
+    gsd
   );
-  registerGraphTools(targetServer, () => vaultIndex, () => vaultPath, () => stateDb);
-  registerWikilinkTools(targetServer, () => vaultIndex, () => vaultPath, () => stateDb);
-  registerQueryTools(targetServer, () => vaultIndex, () => vaultPath, () => stateDb);
-  registerPrimitiveTools(targetServer, () => vaultIndex, () => vaultPath, () => flywheelConfig, () => stateDb);
-  registerGraphAnalysisTools(targetServer, () => vaultIndex, () => vaultPath, () => stateDb, () => flywheelConfig);
-  registerSemanticAnalysisTools(targetServer, () => vaultIndex, () => vaultPath);
-  registerVaultSchemaTools(targetServer, () => vaultIndex, () => vaultPath);
-  registerNoteIntelligenceTools(targetServer, () => vaultIndex, () => vaultPath, () => flywheelConfig);
-  registerMigrationTools(targetServer, () => vaultIndex, () => vaultPath);
-  registerMutationTools(targetServer, () => vaultPath, () => flywheelConfig);
-  registerTaskTools(targetServer, () => vaultPath);
-  registerFrontmatterTools(targetServer, () => vaultPath);
-  registerNoteTools(targetServer, () => vaultPath, () => vaultIndex);
-  registerMoveNoteTools(targetServer, () => vaultPath);
-  registerMergeTools(targetServer, () => vaultPath);
-  registerSystemTools2(targetServer, () => vaultPath);
-  registerPolicyTools(targetServer, () => vaultPath, () => {
-    if (!vaultIndex) return void 0;
-    const index = vaultIndex;
+  registerGraphTools(targetServer, gvi, gvp, gsd);
+  registerWikilinkTools(targetServer, gvi, gvp, gsd);
+  registerQueryTools(targetServer, gvi, gvp, gsd);
+  registerPrimitiveTools(targetServer, gvi, gvp, gcf, gsd);
+  registerGraphAnalysisTools(targetServer, gvi, gvp, gsd, gcf);
+  registerSemanticAnalysisTools(targetServer, gvi, gvp);
+  registerVaultSchemaTools(targetServer, gvi, gvp);
+  registerNoteIntelligenceTools(targetServer, gvi, gvp, gcf);
+  registerMigrationTools(targetServer, gvi, gvp);
+  registerMutationTools(targetServer, gvp, gcf);
+  registerTaskTools(targetServer, gvp);
+  registerFrontmatterTools(targetServer, gvp);
+  registerNoteTools(targetServer, gvp, gvi);
+  registerMoveNoteTools(targetServer, gvp);
+  registerMergeTools(targetServer, gvp);
+  registerSystemTools2(targetServer, gvp);
+  registerPolicyTools(targetServer, gvp, () => {
+    const index = gvi();
+    if (!index) return void 0;
     return ({ query, folder, where, limit = 10 }) => {
       let notes = Array.from(index.notes.values());
       if (folder) {
@@ -21798,42 +22090,42 @@ function registerAllTools(targetServer) {
       }));
     };
   });
-  registerTagTools(targetServer, () => vaultIndex, () => vaultPath);
-  registerWikilinkFeedbackTools(targetServer, () => stateDb);
-  registerCorrectionTools(targetServer, () => stateDb);
-  registerInitTools(targetServer, () => vaultPath, () => stateDb);
+  registerTagTools(targetServer, gvi, gvp);
+  registerWikilinkFeedbackTools(targetServer, gsd);
+  registerCorrectionTools(targetServer, gsd);
+  registerInitTools(targetServer, gvp, gsd);
   registerConfigTools(
     targetServer,
-    () => flywheelConfig,
+    gcf,
     (newConfig) => {
       flywheelConfig = newConfig;
       setWikilinkConfig(newConfig);
     },
-    () => stateDb
+    gsd
   );
-  registerMetricsTools(targetServer, () => vaultIndex, () => stateDb);
-  registerActivityTools(targetServer, () => stateDb, () => {
+  registerMetricsTools(targetServer, gvi, gsd);
+  registerActivityTools(targetServer, gsd, () => {
     try {
       return getSessionId();
     } catch {
       return null;
     }
   });
-  registerSimilarityTools(targetServer, () => vaultIndex, () => vaultPath, () => stateDb);
-  registerSemanticTools(targetServer, () => vaultPath, () => stateDb);
-  registerMergeTools2(targetServer, () => stateDb);
-  registerTemporalAnalysisTools(targetServer, () => vaultIndex, () => vaultPath, () => stateDb);
-  registerMemoryTools(targetServer, () => stateDb);
-  registerRecallTools(targetServer, () => stateDb, () => vaultPath, () => vaultIndex ?? null);
-  registerBriefTools(targetServer, () => stateDb);
-  registerVaultResources(targetServer, () => vaultIndex ?? null);
+  registerSimilarityTools(targetServer, gvi, gvp, gsd);
+  registerSemanticTools(targetServer, gvp, gsd);
+  registerMergeTools2(targetServer, gsd);
+  registerTemporalAnalysisTools(targetServer, gvi, gvp, gsd);
+  registerMemoryTools(targetServer, gsd);
+  registerRecallTools(targetServer, gsd, gvp, () => gvi() ?? null);
+  registerBriefTools(targetServer, gsd);
+  registerVaultResources(targetServer, () => gvi() ?? null);
 }
 function createConfiguredServer() {
   const s = new McpServer(
     { name: "flywheel-memory", version: pkg.version },
     { instructions: generateInstructions(enabledCategories, vaultRegistry) }
   );
-  applyToolGating(s, enabledCategories, () => stateDb, vaultRegistry);
+  applyToolGating(s, enabledCategories, () => stateDb, vaultRegistry, () => vaultPath);
   registerAllTools(s);
   return s;
 }
@@ -21841,7 +22133,7 @@ var server = new McpServer(
   { name: "flywheel-memory", version: pkg.version },
   { instructions: generateInstructions(enabledCategories, vaultRegistry) }
 );
-var _gatingResult = applyToolGating(server, enabledCategories, () => stateDb, vaultRegistry);
+var _gatingResult = applyToolGating(server, enabledCategories, () => stateDb, vaultRegistry, () => vaultPath);
 registerAllTools(server);
 var categoryList = Array.from(enabledCategories).sort().join(", ");
 serverLog("server", `Tool categories: ${categoryList}`);
@@ -21875,6 +22167,20 @@ async function initializeVault(name, vaultPathArg) {
   }
   return ctx;
 }
+function buildVaultScope(ctx) {
+  return {
+    name: ctx.name,
+    vaultPath: ctx.vaultPath,
+    stateDb: ctx.stateDb,
+    flywheelConfig: ctx.flywheelConfig,
+    vaultIndex: ctx.vaultIndex,
+    cooccurrenceIndex: ctx.cooccurrenceIndex,
+    indexState: ctx.indexState,
+    indexError: ctx.indexError,
+    embeddingsBuilding: ctx.embeddingsBuilding,
+    entityEmbeddingsMap: getEntityEmbeddingsMap()
+  };
+}
 function activateVault(ctx) {
   globalThis.__flywheel_active_vault = ctx.name;
   if (ctx.stateDb) {
@@ -21891,16 +22197,7 @@ function activateVault(ctx) {
   setIndexState(ctx.indexState);
   setIndexError(ctx.indexError);
   setEmbeddingsBuilding(ctx.embeddingsBuilding);
-  setActiveScope({
-    name: ctx.name,
-    vaultPath: ctx.vaultPath,
-    stateDb: ctx.stateDb,
-    flywheelConfig: ctx.flywheelConfig,
-    cooccurrenceIndex: ctx.cooccurrenceIndex,
-    indexState: ctx.indexState,
-    indexError: ctx.indexError,
-    embeddingsBuilding: ctx.embeddingsBuilding
-  });
+  setActiveScope(buildVaultScope(ctx));
 }
 function getActiveVaultContext() {
   if (!vaultRegistry) return null;
@@ -21967,6 +22264,10 @@ async function main() {
     const { createMcpExpressApp } = await import("@modelcontextprotocol/sdk/server/express.js");
     const { StreamableHTTPServerTransport } = await import("@modelcontextprotocol/sdk/server/streamableHttp.js");
     const httpPort = parseInt(process.env.FLYWHEEL_HTTP_PORT ?? "3111", 10);
+    if (!Number.isFinite(httpPort) || httpPort < 1 || httpPort > 65535) {
+      console.error(`[flywheel] Fatal: invalid FLYWHEEL_HTTP_PORT: ${process.env.FLYWHEEL_HTTP_PORT} (must be 1-65535)`);
+      process.exit(1);
+    }
     const httpHost = process.env.FLYWHEEL_HTTP_HOST ?? "127.0.0.1";
     const app = createMcpExpressApp({ host: httpHost });
     app.post("/mcp", async (req, res) => {
@@ -22139,6 +22440,7 @@ function runPeriodicMaintenance(db4) {
     purgeOldSuggestionEvents(db4, 30);
     purgeOldNoteLinkHistory(db4, 90);
     purgeOldSnapshots(db4, 90);
+    pruneStaleRetrievalCooccurrence(db4, 30);
     lastPurgeAt = now;
     serverLog("server", "Daily purge complete");
   }
@@ -23012,6 +23314,21 @@ async function runPostIndexWork(index) {
           tracker.end({ error: String(e) });
           serverLog("watcher", `Tag scan: failed: ${e}`, "error");
         }
+        tracker.start("retrieval_cooccurrence", {});
+        try {
+          if (stateDb) {
+            const inserted = mineRetrievalCooccurrence(stateDb);
+            tracker.end({ pairs_inserted: inserted });
+            if (inserted > 0) {
+              serverLog("watcher", `Retrieval co-occurrence: ${inserted} new pairs`);
+            }
+          } else {
+            tracker.end({ skipped: "no stateDb" });
+          }
+        } catch (e) {
+          tracker.end({ error: String(e) });
+          serverLog("watcher", `Retrieval co-occurrence: failed: ${e}`, "error");
+        }
         const duration = Date.now() - batchStart;
         if (stateDb) {
           recordIndexEvent(stateDb, {